When i native installed gentoo, I had to manually type each folder in usr before the transfer from loopback would work. a small shell script that cp's each folder and waits 10 seconds between each would be ideal and might have more success.

It's a known issue and it shouldn't be the case. In earlier releases, the copy worked fine. For some reason with the latest release(s), there's an issue that causes crashes during copy. There's several other threads about it.